SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 35
Search took 0.00 seconds.
Search: Posts Made By: Macspider
Forum: Bioinformatics 01-30-2018, 02:09 AM
Replies: 98
Views: 26,239
Posted By Macspider
Hi Brian, After reading this whole thread,...

Hi Brian,

After reading this whole thread, I still have some doubts about how the mode=extend works in tadpole.

My understanding is: kmers of size k are extracted from the reads and, upon...
Forum: Bioinformatics 03-03-2017, 03:44 AM
Replies: 10
Views: 2,234
Posted By Macspider
Yes, I solved it in the end. Unluckily for you,...

Yes, I solved it in the end. Unluckily for you, there isn't a clear reason why it worked in the end, but it did. How I did it:

1 - went to the root directory (/)

2 - downloaded the jksrc.zip...
Forum: Bioinformatics 11-10-2016, 04:13 AM
Replies: 10
Views: 4,700
Posted By Macspider
Hi, I came to this post just now: I'm...

Hi,

I came to this post just now: I'm working on benthamiana too, calling variants and had the same question in my head. Since you asked this quite a time ago, maybe could you add up how you...
Forum: Bioinformatics 11-10-2016, 01:35 AM
Replies: 2
Views: 1,598
Posted By Macspider
As a side note, the reason why you sequence one...

As a side note, the reason why you sequence one sample more than once is that you usually do want to have some replicates, i.e. statistical power in the subsequent analyses. This doesn't apply to...
Forum: Bioinformatics 10-31-2016, 07:08 AM
Replies: 2
Views: 2,423
Posted By Macspider
Hi, I know how. First, quoting the...

Hi, I know how.
First, quoting the hisat2-align manual you will read that:



Since GFF / GTF files are usually prone to mis-formatting errors given that for a long time there has been no...
Forum: Bioinformatics 10-31-2016, 05:45 AM
Replies: 0
Views: 674
Posted By Macspider
How likely is that Augustus mis-predicts a UTR region?

Hi all,

I'm working with a gene set that I generated with Augustus 3.2.1 and that has an overall high quality. However, I was unlucky and the exact gene that I was hoping to find as it should be...
Forum: Bioinformatics 08-23-2016, 11:49 PM
Replies: 19
Views: 2,929
Posted By Macspider
It looks like you still don't map more than 20%...

It looks like you still don't map more than 20% or your reads though... Maybe you didn't trim them correctly? How did you do the trimming process? Maybe they still contain some adapter sequences and...
Forum: Bioinformatics 08-23-2016, 08:08 AM
Replies: 19
Views: 2,929
Posted By Macspider
I'm not sure about this. Because the...

I'm not sure about this. Because the supernumerarity itself doesn't affect the alignment if the sequence is the same for each supernumerary chromosome. If the sequence diverges, then you lose a lot...
Forum: Bioinformatics 08-23-2016, 07:15 AM
Replies: 19
Views: 2,929
Posted By Macspider
I am surprised by the fact that bowtie2 maps ~...

I am surprised by the fact that bowtie2 maps ~ 70% of the data while bowtie maps only 45%. I think you should really make a list of all the parameters that bowtie2 applies by default and see which...
Forum: Bioinformatics 08-23-2016, 12:33 AM
Replies: 6
Views: 1,968
Posted By Macspider
For what concerns me, I didn't use many of these...

For what concerns me, I didn't use many of these but for the ones I used, Thumbs up for Geneious Pro and Mathematica.
Forum: Bioinformatics 08-23-2016, 12:27 AM
Replies: 14
Views: 14,827
Posted By Macspider
Yes, it is a bug in TopHat. Didn't they fix it in...

Yes, it is a bug in TopHat. Didn't they fix it in TopHat2? I recently used it and the flags were alright.
Forum: Bioinformatics 08-23-2016, 12:22 AM
Replies: 33
Views: 3,897
Posted By Macspider
If you exported the RepeatScout-1 directory to...

If you exported the RepeatScout-1 directory to your $PATH, you don't need to write ./filename.prl, you just need to write filename.prl. If you include "./", it will search it in the current directory...
Forum: Bioinformatics 08-23-2016, 12:12 AM
Replies: 19
Views: 2,929
Posted By Macspider
Before reaching out to the authors, I'd suggest...

Before reaching out to the authors, I'd suggest that you post here the BOWTIE command you ran (there must be somethign in the trinity log), to add info on the one from trinity you posted.
- How many...
Forum: Bioinformatics 08-23-2016, 12:04 AM
Replies: 2
Views: 1,543
Posted By Macspider
Hey, First, when you make and it throws out...

Hey,
First, when you make and it throws out warnings like unused-value, it doesn't mean that it automatically doesn't work (it can be). Sometimes these are warnings because some of the dependencies...
Forum: Bioinformatics 08-17-2016, 05:28 AM
Replies: 2
Views: 1,401
Posted By Macspider
I'm not an expert on PacBio data, but I think you...

I'm not an expert on PacBio data, but I think you can hardly determine if they are polycistronic or not without a reference genome.
With coding region predictors you can only guess which parts of...
Forum: Bioinformatics 08-17-2016, 05:15 AM
Replies: 1
Views: 1,983
Posted By Macspider
Super late about this, but since I'm having this...

Super late about this, but since I'm having this same problem of yours, I just figured out that basically what the bam2hints script in the augustus/scripts folder does is exactly what you ask here,...
Forum: Bioinformatics 08-04-2016, 03:21 AM
Replies: 3
Views: 1,992
Posted By Macspider
Yep, exactly how I did. :) I have other...

Yep, exactly how I did. :)
I have other problems with BRAKER1, fancy take a look? Maybe you know:
http://seqanswers.com/forums/showthread.php?p=197504#post197504
Forum: Bioinformatics 08-04-2016, 03:12 AM
Replies: 0
Views: 1,119
Posted By Macspider
BRAKER1 crashes due to "invalid regression data"

This is what my BRAKER1 run throws out when crashing:

failed to execute: perl /software/genemark/GeneMark_ES_ET_4.32/gmes_petap.pl --sequence=/../genome.fa --ET=/../hintsfile.gff...
Forum: Academic/Non-Profit Jobs 08-04-2016, 12:59 AM
Replies: 0
Views: 865
Posted By Macspider
Open Ph.D position in Bioinformatics @ BOKU, Vienna (AT)

Hi all,

The group I work in, lead by Univ.Prof. Mag. Dr. Heinz Himmelbauer ( http://www.ncbi.nlm.nih.gov/pubmed/?term=Heinz+Himmelbauer ) is offering a PhD position in Bioinformatics, advertised...
Forum: Bioinformatics 08-04-2016, 12:48 AM
Replies: 3
Views: 1,992
Posted By Macspider
I solved it trying the solutions suggested here. ...

I solved it trying the solutions suggested here.
https://gist.github.com/macmanes/bc5598e0d079ff6d71f2
Forum: Bioinformatics 08-04-2016, 12:40 AM
Replies: 1
Views: 1,883
Posted By Macspider
I know it's been a while, but I've been recently...

I know it's been a while, but I've been recently through the same error and I solved it trying the solutions suggested here.
https://gist.github.com/macmanes/bc5598e0d079ff6d71f2

Have you by...
Forum: Bioinformatics 07-20-2016, 07:59 AM
Replies: 3
Views: 1,992
Posted By Macspider
BRAKER1 fails: inappropriate ioctl for device

Hi all, I'm having a problem which is more linux related than biology related. I'm running the BRAKER1 pipeline (which involves Augustus and Gene-mark ET) for a gene prediction, and I'm getting back...
Forum: RNA Sequencing 07-20-2016, 07:51 AM
Replies: 2
Views: 1,028
Posted By Macspider
Totally agree. Using FPKM or RPKM in this case...

Totally agree. Using FPKM or RPKM in this case can be done because cufflinks outputs it automatically in the isoforms.fpkm_tracking file so you don't bother using other units.
What you need is to...
Forum: Bioinformatics 07-20-2016, 07:33 AM
Replies: 2
Views: 1,950
Posted By Macspider
It's a bit late for this answer but maybe future...

It's a bit late for this answer but maybe future users will benefit from that:
When you use FPKM / RPKM as a measure unit you already have a normalized unit, which accounts for the gene length....
Forum: Illumina/Solexa 07-20-2016, 07:19 AM
Replies: 2
Views: 988
Posted By Macspider
Before merging them I would go with some...

Before merging them I would go with some statistical test to see their closeness. For example, run cufflinks on both separately and then do a principal component analysis (PCA) with R to see how...
Showing results 1 to 25 of 35

 


All times are GMT -8. The time now is 05:04 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO